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Copper in PDB 6zaw: Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography

Enzymatic activity of Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography

All present enzymatic activity of Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography:
1.7.2.1;

Protein crystallography data

The structure of Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography, PDB code: 6zaw was solved by S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.87 / 1.30
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 106.87, 106.87, 106.87, 90, 90, 90
R / Rfree (%) 13.5 / 18

Copper Binding Sites:

The binding sites of Copper atom in the Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography (pdb code 6zaw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography, PDB code: 6zaw:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 6zaw

Go back to Copper Binding Sites List in 6zaw
Copper binding site 1 out of 2 in the Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:16.1
occ:0.90
 ND1 A:HIS89 2.0 14.4 1.0
ND1 A:HIS140 2.1 15.5 1.0
SG A:CYS130 2.2 14.8 1.0
SD A:MET145 2.5 16.8 1.0
CE1 A:HIS140 2.9 19.0 1.0
CE1 A:HIS89 3.0 16.3 1.0
CG A:HIS89 3.1 14.1 1.0
CG A:HIS140 3.1 16.2 1.0
CB A:CYS130 3.2 14.8 1.0
CE A:MET145 3.3 17.1 1.0
CB A:HIS89 3.5 14.9 1.0
CB A:HIS140 3.5 14.8 1.0
CA A:HIS89 3.8 15.7 1.0
CG A:MET145 3.9 15.5 1.0
NE2 A:HIS140 4.1 18.7 1.0
NE2 A:HIS89 4.1 15.8 1.0
CG A:PRO132 4.2 18.5 1.0
CD2 A:HIS140 4.2 19.0 1.0
CD2 A:HIS89 4.2 15.4 1.0
O A:PRO88 4.3 16.9 1.0
CB A:MET145 4.4 15.4 1.0
CA A:CYS130 4.6 14.1 1.0
CD A:PRO132 4.6 16.4 1.0
N A:ASN90 4.7 15.5 1.0
CA A:HIS140 4.7 13.4 1.0
N A:HIS89 4.8 16.1 1.0
C A:HIS89 4.8 15.4 1.0
CE A:MET56 4.9 15.0 1.0
C A:PRO88 5.0 16.7 1.0

Copper binding site 2 out of 2 in 6zaw

Go back to Copper Binding Sites List in 6zaw
Copper binding site 2 out of 2 in the Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Damage-Free No-Bound Copper Nitrite Reductase From Bradyrhizobium Sp. Ors 375 (Two-Domain) Determined By Serial Femtosecond Rotation Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:13.8
occ:0.90
 NE2 A:HIS129 2.0 13.4 1.0
NE2 A:HIS94 2.0 11.8 1.0
O A:HOH505 2.1 25.0 0.3
O A:NO410 2.1 25.9 0.4
N A:NO410 2.5 25.3 0.4
CD2 A:HIS129 2.9 13.7 1.0
CE1 A:HIS94 2.9 11.4 1.0
CE1 A:HIS129 3.0 12.9 1.0
CD2 A:HIS94 3.1 12.3 1.0
OD2 A:ASP92 3.6 26.6 1.0
ND1 A:HIS94 4.1 12.5 1.0
CG A:HIS129 4.1 13.7 1.0
ND1 A:HIS129 4.1 13.2 1.0
CG A:HIS94 4.2 10.8 1.0
O A:HOH503 4.2 29.5 0.5
CG A:ASP92 4.3 20.6 1.0
O A:HOH509 4.4 27.8 1.0
OD1 A:ASP92 4.7 20.5 1.0
O A:HOH798 5.0 15.6 1.0

Reference:

S.L.Rose, S.V.Antonyuk, D.Sasaki, K.Yamashita, K.Hirata, G.Ueno, H.Ago, R.R.Eady, T.Tosha, M.Yamamoto, S.S.Hasnain. An Unprecedented Insight Into the Catalytic Mechanism of Copper Nitrite Reductase From Atomic-Resolution and Damage-Free Structures Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABD8523
Page generated: Wed Jul 31 07:58:42 2024

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